Well there is the obvious answer, that the libraries are very different and often incompatible with each other, but since GNOME 3 uses the newer libraries that is preferable. At this point considering the work that has gone into Gnome Classic for 12.04, I would say no, that there isn't really much of a difference at this point. Maybe a few taskbar applets that haven't been ported yet, but aside from that there isn't really much point in using Gnome 2 anymore.

Article here from OMGUbuntu showing the Gnome Classic mode in 12.04